Founded in 1916, Real Club Deportivo Mallorca was initially named Junta Directiva del Alfonso XIII after the King of Spain. The team name was changed to Club Deportivo Mallorca for political reasons in 1931, before the club was granted royal patronage in 1949. As a result, the team's name gained the 'Real' or 'Royal' prefix it has today.

The club made its first appearance in the Primera División in the 1960-61 season. Since that time, the club has bounced between the first, second and third tiers of the Spanish league system.

Recently, the club has been through its most successful period, maintaining its top flight status from the 1997-98 season until the present day. After finishing as runners up for the Copa del Rey in 1997-98, the club went one better in 2002-03, defeating Recreativo de Huelva 3-0 in the final to lift the trophy. During this period, Mallorca also reached the final of the last ever UEFA Cup Winners' Cup, ultimately losing to Lazio in the final. The club's best ever league performance was a third place finish in the 2000–01 season behind Deportivo La Coruna and champions, Valencia.

Legendary players to represent the club include former Spanish international Miguel Ángel Nadal, who made 255 appearances during his two spells at Mallorca, and Samuel Eto'o, who spent five seasons at the club, becoming Mallorca's greatest ever league goal scorer with 54 league goals.

Since 1999, the team has played its home matches at the The Iberostar Stadium. Previously known as the Son Moix, it has a capacity of 23,142 and is the biggest stadium on the Balearic Islands. In recent years, the club has explored the possibility of expanding the stadium to a 40,000 seater capacity, although those plans appear to be on hold. More recently, Mallorca have proposed a new 40,000 seater stadium as part of the Estudio Lamela project.